48 lines
1.5 KiB
Bash
Executable File
48 lines
1.5 KiB
Bash
Executable File
#!/bin/bash
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# Script name: run_pH_analysis_pipeline.sh
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# Function: Combine InterPro annotation and pH prediction into one pipeline
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# Usage: ./run_pH_analysis_pipeline.sh <prokka_annotation_dir>
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# Example: ./run_pH_analysis_pipeline.sh ./prokka_annotation
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# Check input parameter (must be 1: prokka annotation directory)
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if [ $# -ne 2 ]; then
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echo "Error: Incorrect number of arguments!"
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echo "Usage: $0 <prokka_annotation_dir> <ph_predict_dir>"
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echo "Example: $0 ./prokka_annotation ./ph_predict_dir"
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exit 1
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fi
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PROKKA_DIR="$1"
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output_dir="$2"
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mkdir -p "$output_dir" || {
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echo "Error: Failed to create output directory $output_dir!"
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exit 1
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}
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# Step 1: Run InterPro annotation script
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echo "=== Step 1: Starting InterPro annotation ==="
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if [ -f "/app/scripts/pfam_annotation.sh" ]; then
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bash /app/scripts/pfam_annotation.sh "$PROKKA_DIR" "$output_dir"|| {
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echo "Error: pfam_annotation.sh execution failed!"
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exit 1
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}
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else
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echo "Error: pfam_annotation.sh not found in current directory!"
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exit 1
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fi
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# Step 2: Run pH prediction Python script
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echo -e "\n=== Step 2: Starting pH model prediction ==="
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if [ -f "/app/scripts/pHmodel.py" ]; then
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# Assume pHmodel.py takes two parameters: input dir (.) and output dir (.) as in original command
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python /app/scripts/pHmodel.py "$output_dir" "$output_dir" || {
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echo "Error: pHmodel.py execution failed!"
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exit 1
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}
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else
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echo "Error: pHmodel.py not found in current directory!"
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exit 1
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fi
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echo -e "\n=== All steps completed successfully ===" |